tsy19900929 / snpefftomaf Goto Github PK

Hello,

snpeffToMaf doesn't correctly determine the End_Position or the Variant_Type for mutations greater than one base. For example,

Gene Start_Position End_Position Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1
FLG 152308531 152218985 missense_variant SNP AA AA

Hi @tsy19900929,

Thanks for developing this utility. I have some VCF with germline variant calls generated from Strelka. I used SnpEff to annotate my VCFs. I'm running into some errors while converting my VCF to MAF.

Use of uninitialized value $minDP in numeric lt (<) at snpeffToMaf.pl line 51, <INFILE> line 3412. Argument "LowGQX" isn't numeric in numeric lt (<) at snpeffToMaf.pl line 51, <INFILE> line 3412. Illegal division by zero at snpeffToMaf.pl line 53, <INFILE> line 3412.

Any suggestions on how to fix this ? Thanks.

Hello, I would just like to know if this tool works for snpeff outputs where the rows have multiple annotations?

@tsy19900929 Hi, I have changed the FORMAT parameter, but this error still occurs.

.

ls $data_dir/*.anno.vcf |while read id; do nohup perl snpeffToMaf.pl $id 100 0.05 & done

if i set 100 for minimum depth, only can get 33 gene mutations for one sample.
i try 10,20,30,40,50,60,70,80,90, each of them can get more than 10000 gene mutaitons

Hello,

Does this tool also work on VCF files that have been annotated with SNPsift?

I'm using it with a SNPeff and SNPsift annotated VCF file. This is my command. It gives me a Maf file but also the following errors.
perl /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl JMT1-9.anno_somaticStrict.sort.vcf > test.maf

This gives me:
Use of uninitialized value $minDP in numeric lt (<) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 51, line 185.
Argument "18:134:0.134:20:-48.2396" isn't numeric in division (/) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 53, line 185.
Use of uninitialized value $minAF in numeric lt (<) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 54, line 185.
Use of uninitialized value $minDP in numeric lt (<) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 51, line 186.
Argument "31:138:0.225:20:-100" isn't numeric in division (/) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 53, line 186.
Use of uninitialized value $minAF in numeric lt (<) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 54, line 186.
Use of uninitialized value $minDP in numeric lt (<) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 51, line 187.
Argument "14:68:0.206:20:-34.7853" isn't numeric in division (/) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 53, line 187.
Use of uninitialized value $minAF in numeric lt (<) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 54, line 187.
Use of uninitialized value $minDP in numeric lt (<) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 51, line 188.
Argument "15:93:0.161:20:-60.5661" isn't numeric in division (/) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 53, line 188.
Use of uninitialized value $minAF in numeric lt (<) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 54, line 188.
Use of uninitialized value $minDP in numeric lt (<) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 51, line 189.
Argument "23:110:0.209:20:-44.5066" isn't numeric in division (/) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 53, line 189.
Use of uninitialized value $minAF in numeric lt (<) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 54, line 189.
Use of uninitialized value $minDP in numeric lt (<) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 51, line 190.
Argument "7:24:0.292:20:-10.2153" isn't numeric in division (/) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 53, line 190.
Use of uninitialized value $minAF in numeric lt (<) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 54, line 190.
Use of uninitialized value $minDP in numeric lt (<) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 51, line 191.
Argument "8:50:0.16:20:-34.2018" isn't numeric in division (/) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 53, line 191.
Use of uninitialized value $minAF in numeric lt (<) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 54, line 191.
Use of uninitialized value $minDP in numeric lt (<) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 51, line 192.
Argument "8:21:0.381:20:-46.9751" isn't numeric in division (/) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 53, line 192.
Use of uninitialized value $minAF in numeric lt (<) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 54, line 192.
Use of uninitialized value $minDP in numeric lt (<) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 51, line 193.
Argument "39:76:0.513:20:-100" isn't numeric in division (/) at /home/kam9898/snpeffToMaf-master/snpeffToMaf.pl line 53, line 193.